Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer
| Autor: | Sundaram Suresh, Saras Saraswathi, Andrzej Kloczkowski, Vasiliy Sachnev, Rashid Niaz |
|---|---|
| Přispěvatelé: | School of Computer Engineering |
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Candidate gene
Extreme learning machine 02 engineering and technology Biology Global cancer map Bioinformatics Biochemistry Hallmarks of cancer Pattern Recognition Automated 03 medical and health sciences Artificial Intelligence Structural Biology Neoplasms Science::Medicine::Biomedical engineering [DRNTU] Biomarkers Tumor 0202 electrical engineering electronic engineering information engineering Humans Molecular Biology Oligonucleotide Array Sequence Analysis 030304 developmental biology Binary coded genetic algorithm 0303 health sciences Artificial neural network Applied Mathematics 3. Good health Computer Science Applications Gene Expression Regulation Neoplastic The Hallmarks of Cancer YWHAZ Cancer biomarkers 020201 artificial intelligence & image processing Neural Networks Computer DNA microarray Classifier (UML) Algorithms Research Article |
| Zdroj: | BMC Bioinformatics |
| Popis: | Background Traditional cancer treatments have centered on cytotoxic drugs and general purpose chemotherapy that may not be tailored to treat specific cancers. Identification of molecular markers that are related to different types of cancers might lead to discovery of drugs that are patient and disease specific. This study aims to use microarray gene expression cancer data to identify biomarkers that are indicative of different types of cancers. Our aim is to provide a multi-class cancer classifier that can simultaneously differentiate between cancers and identify type-specific biomarkers, through the application of the Binary Coded Genetic Algorithm (BCGA) and a neural network based Extreme Learning Machine (ELM) algorithm. Results BCGA and ELM are combined and used to select a subset of genes that are present in the Global Cancer Mapping (GCM) data set. This set of candidate genes contains over 52 biomarkers that are related to multiple cancers, according to the literature. They include APOA1, VEGFC, YWHAZ, B2M, EIF2S1, CCR9 and many other genes that have been associated with the hallmarks of cancer. BCGA-ELM is tested on several cancer data sets and the results are compared to other classification methods. BCGA-ELM compares or exceeds other algorithms in terms of accuracy. We were also able to show that over 50% of genes selected by BCGA-ELM on GCM data are cancer related biomarkers. Conclusions We were able to simultaneously differentiate between 14 different types of cancers, using only 92 genes, to achieve a multi-class classification accuracy of 95.4% which is between 21.6% and 38% higher than other results in the literature for multi-class cancer classification. Our findings suggest that computational algorithms such as BCGA-ELM can facilitate biomarker-driven integrated cancer research that can lead to a detailed understanding of the complexities of cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0565-5) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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